## [1] "O77_p5_con_R1_2.hicup.bam"
Truncation & Mapping
Truncation Frequency
| Total |
67,469,988 |
67,469,988 |
| Not Truncated |
38,790,372 |
36,700,618 |
| Truncated |
28,679,616 |
30,769,370 |
Truncated Read Length
| Average Length Truncated |
47.2 |
47.1 |
Mapping Efficiency
| Too Short To Map |
5,024,738 |
5,126,162 |
| Unique Alignments |
57,419,111 |
55,772,438 |
| Multiple Alignments |
2,464,572 |
2,499,157 |
| Failed To Align |
2,561,567 |
4,072,231 |
| Paired |
47,765,077 |
47,765,077 |
Truncation and Mapping Bar Plot
Filtering
Filtering Breakdown by Category
| Valid Pairs |
25,870,377 |
| Invalid Pairs |
21,894,700 |
| Same Circularised |
1,380 |
| Same Dangling Ends |
4,788,107 |
| Same Fragment Internal |
8,648,239 |
| Re Ligation |
6,094,287 |
| Contiguous Sequence |
104,180 |
| Wrong Size |
2,258,507 |
| Total Pairs |
47,765,077 |
Filtering Breakdown Pie Chart
Ditag Length Distribution
Deduplication
Deduplication Summary Table
| Read Pairs |
25,870,377 |
31,333 |
| Cis-close (<10Kbp) |
2,744,526 |
2,943 |
| Cis-far (>10Kbp) |
17,448,078 |
17,104 |
| Trans |
5,677,773 |
11,286 |
Deduplication Bar Chart
Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data
